SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q8MJ06 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MSDTPSTGFSIIHPTSSEDQVPPPRHLSLTHPVVAKRISFYKSGDPQFGG    50
  51  VRVVVNPRSFKSFDALLDNLSRKVPLPFGVRNISTPRGRHSITRLEELED   100
 101  GESYLCSHGRKVQPVDLDKARRRPRPWLSSRAISAQAPPHPVAVAAPGKP   150
 151  RAPRSLVVFRNGDPKTRRTVLLSRRVTQSFEAFLQHLTEVMQRPVVKLYA   200
 201  TDGRRVPSLQAVILSSGAVVAAGREPFKPGNYDIQKYLLPARLPGISQRV   250
 251  YPKGNAKSESRKISTHMSSSSRSQIYSVSSEKTHNNDCYLDYSFVPENYL   300
 301  ALEKSDSQNLPIYPSEDDIEKSIIFNQDGTMTVEMKVRFRIKEEETIKWT   350
 351  TTVSKTGPSNNDEKSEMSFPGRTESRSSGLKLAACSFSADVSPMERSSDQ   400
 401  EGSLPEEINIQTTDEEAETCSSASWENATVDTDITQGTQDQAKHRFYRPP   450
 451  TPGLRRVRQKKSVIGSVTLVSETEVQEKMIGQFSYSEERESGENKSEYHM   500
 501  FAHSCSKMSAVSNKPVLVQINNNDQMEESLLERKKENRLLKSSAISAGVI   550
 551  EITSQKMLEMSHNNGLPSTISNNSIVEEGVVDSMVSDNKTGIKNFRAYDN   600
 601  TNDRFSPISADATHFSSTNSGTDKNISEATASETSSTVTARIDRLINEFA   650
 651  QCGLTKLPKNEKKILSSVASKKKKKSLQQAINSRYQDGQLATKGILNKNE   700
 701  RINTRGRIRKEMILQDSDSRLKGGILCEEDLQTSDTVIESNTFCSKSNLN   750
 751  SMISKNFHRNKLNTTQNSKVQGLLTKRKSKSLKKVSLGAPKKREICQGDK   800
 801  VFPHNESKYCKSTFENKSLFHVFNILEQKPKYFYAPQSQAEVASGYLRGM   850
 851  AKKSLVTDSHITLRSQKKQKGDKLKASAVVSKQHATTRANSLASLKKPDF   900
 901  PEDIAHHSVQNYIQSWLQNINPYPTLKPIKSAPVCRNEMSVVNCNNNSFP   950
 951  GNDPHKSSGKINNFVMESNKHITKIASLTGDNLCKEGDKSFIASDTGEED  1000
1001  LHETQVGSLNDAYLVSLHEHCTLSQSAINDRNTKRHIAAEKSGPEKKLVY  1050
1051  QEINLARKRQSVEAAIQVDPIEEETPKDLLPVLMLHQLQASVPGISKTQN  1100
1101  GVVQMPGSLANVPFHSAICNSSTNLLLAWLLVLNLKGSMNSFCQVDAHKT  1150
1151  INKSSETLALLEILKHIAITEEADDLKAAVANLVESTTSHFGLSEKEQDV  1200
1201  VPLDLSANCSTVSIQSVPKCSENERTQRISSLDGDCSASEACAPEVCVLE  1250
1251  VTCSPCETWTVNKTYPPKETCNPSDTHFPSDGYGVDQTSMNKACFLGEVC  1300
1301  SLTDTVFSNKACAQKENHIYEGACPTVETYVPVSVCNTIDFFNSKENTYT  1350
1351  DNLESTEELERGDDIQKDLNILTDPEYKNGFNTLVSHQNVSNLSSCRLCL  1400
1401  SEKEAELDKKHSSLDDFKNCSLKKFQDENAYTSFDMEEPRTSEEPGSITN  1450
1451  SMTSSERNISELESFEELENPDTDIFNTVVNGGEQATEELIQEELEASKT  1500
1501  LELIDISGKNVMEEKRRNGIIYEIISKRLATPPSLVFCYDSKQNREKETN  1550
1551  EGETKMVKMMVKSMEAGSYSESSPDLKKCIKSPVTSDWSDYRPDSDSEQP  1600
1601  YKTSSDDPNDSGELAQEKEYNIGFVKRAIEKLYGKADIIKPSFFPGSTRK  1650
1651  SQVCPYNSVEFQCSRKASLYDSEGQSFGSSEQVSTSSPMLQEFQEERQDK  1700
1701  CDVNGVRNDYYGGDIVEPGTKQNDHSRILTDIEEGVLIDKGKWLLKENHL  1750
1751  LRMSSENPGMCGNADTTSVDTLLDNNSSEVPYSHFGNLAPVPVMDELSSS  1800
1801  ELEELTQPLELKCNYFNMPHGSDSEPFHEDVHNETCAKERIANHHTEERG  1850
1851  NNHQSERVCTSVTHSFTSASNKVYPVSDDAIKNQPLPGSNMIHGTLQEAD  1900
1901  SLDKLYALCGQHCPILTVIIQPVNEEDRGFAYRKESDIENFLGFYLWMKI  1950
1951  HPYLLQTDKKVFREENNKASMRQNHIDNAIGDIFDQFYFNNTFDLMGKRR  2000
2001  KQKRINFLELEEEGNLKKFQPDLKERLCMNFLHTSLLVVSNMNSDTQDLS  2050
2051  SQTNEMFKAVDENNNLLNTGFQGSRTNLNQIVRENTNCHYFFEMLGQACL  2100
2101  LDICQVETSLNISNRNTLEELCMFEGENLFIWEEEDILNLTDLESSREQE  2150
2151  DL                                                  2152

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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